## [1] "data/config.vertebrata_minimal.yaml"

Analysis report - 24 January, 2023 - 21:33 CET - version: 0.9.7

Setup

Location of genomes files:

results/assemblies

Total number of included genomes: 25
Locally provided genomes: 1
Successfully downloaded genomes: 24
Failed species downloads: 0
Not downloaded:

Information on successfully downloaded genomes:

info <- ""
if (file.exists(downloaded_genomes_statistics_file))
{
  if (file.size(downloaded_genomes_statistics_file) != 0) {
      data <- read.csv(downloaded_genomes_statistics_file, sep="\t", header=T)
  } else {
    info <- "*No information about downloaded genomes found. Maybe you only have local species?*"
  }
  
  data %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px") # %>% mutate(ftp_path = cell_spec("download", "html", link = ftp_path)) %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px")
} else {
  info <- "*No information about downloaded genomes found. Did you run phylociraptor setup ?*"
}
name id assembly_accession bioproject biosample wgs_master refseq_category taxid species_taxid organism_name infraspecific_name isolate version_status assembly_level release_type genome_rep seq_rel_date asm_name submitter gbrs_paired_asm paired_asm_comp ftp_path excluded_from_refseq relation_to_type_material
Amblyraja_radiata 529558 GCA_010909765.2 PRJNA591369 SAMN09948523 JAAGWR000000000.1 representative genome 386614 386614 Amblyraja radiata CabotCenter1 latest Chromosome Minor Full 2020/02/21 sAmbRad1.1.pri Vertebrate Genomes Project GCF_010909765.2 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/909/765/GCA_010909765.2_sAmbRad1.1.pri NA na
Anolis_carolinensis 1121 GCA_000090745.2 PRJNA18787 SAMN02981230 AAWZ00000000.2 representative genome 28377 28377 Anolis carolinensis latest Chromosome Minor Full 2011/01/10 AnoCar2.0 Broad Institute GCF_000090745.1 identical https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/090/745/GCA_000090745.2_AnoCar2.0 NA na
Callorhinchus_milii 2221 GCA_000165045.2 PRJNA18361 SAMN00000800 AAVX00000000.2 na 7868 7868 Callorhinchus milii IMCB2004 latest Scaffold Major Full 2013/12/11 Callorhinchus_milii-6.1.3 Institute of Molecular and Cell Biology, Singapore GCF_000165045.1 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/165/045/GCA_000165045.2_Callorhinchus_milii-6.1.3 superseded by newer assembly for species NA na
Canis_lupus 1488310 GCA_905319855.2 PRJEB43200 SAMEA7532739 CAJNRB000000000.2 na 9612 9612 Canis lupus latest Chromosome Major Full 2021/03/26 mCanLor1.2 WELLCOME SANGER INSTITUTE na na https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/319/855/GCA_905319855.2_mCanLor1.2 NA na
Danio_kyathit 1465680 GCA_903798195.1 PRJEB38580 SAMEA104130240 CAIGQS000000000.1 representative genome 242068 242068 Danio kyathit latest Chromosome Major Full 2020/06/27 fDanKya3.1 SC na na https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/798/195/GCA_903798195.1_fDanKya3.1 NA na
Dasypus_novemcinctus 3904 GCA_000208655.2 PRJNA12594 SAMN02953623 na na 9361 9361 Dasypus novemcinctus 3-136 replaced Scaffold Major Full na na Baylor College of Medicine GCF_000208655.3 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/208/655/GCA_000208655.2_Dasnov3.0 NA na
Eptatretus_burgeri 1396691 GCA_900186335.2 PRJEB21290 SAMEA104124530 FYBX00000000.2 na 7764 7764 Eptatretus burgeri latest Scaffold Major Full 2017/10/24 Eburgeri_3.2 RIKEN CENTER FOR DEVELOPMENTAL BIOLOGY na na https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/186/335/GCA_900186335.2_Eburgeri_3.2 NA na
Gallus_gallus 815795 GCA_016699485.1 PRJNA660757 SAMN15960293 JAENSK000000000.1 representative genome 9031 9031 Gallus gallus breed=Cross of Broiler mother + white leghorn layer father bGalGal1 latest Chromosome Major Full 2021/01/19 bGalGal1.mat.broiler.GRCg7b Vertebrate Genomes Project GCF_016699485.2 identical https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/699/485/GCA_016699485.1_bGalGal1.mat.broiler.GRCg7b NA na
Homo_sapiens 1 GCA_000001405.28 PRJNA31257 na na 9606 9606 Homo sapiens replaced Chromosome Patch Full na na Genome Reference Consortium GCF_000001405.40 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13 NA na
Latimeria_chalumnae 4626 GCA_000225785.1 PRJNA56111 SAMN00138723 AFYH00000000.1 representative genome 7897 7897 Latimeria chalumnae SAIAB 97564 latest Scaffold Major Full 2011/09/12 LatCha1 Broad Institute GCF_000225785.1 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/225/785/GCA_000225785.1_LatCha1 NA na
Loxodonta_africana 8 GCA_000001905.1 PRJNA12569 SAMN02953622 AAGU00000000.3 representative genome 9785 9785 Loxodonta africana ISIS603380 latest Scaffold Major Full 2009/07/15 Loxafr3.0 Broad Institute GCF_000001905.1 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/905/GCA_000001905.1_Loxafr3.0 NA na
Meleagris_gallopavo 1361 GCA_000146605.4 PRJNA42129 SAMN02981253 ADDD00000000.2 representative genome 9103 9103 Meleagris gallopavo breed=Aviagen turkey brand Nicholas breeding stock NT-WF06-2002-E0010 latest Chromosome Minor Full 2019/10/21 Turkey_5.1 Turkey Genome Consortium GCF_000146605.3 identical https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/146/605/GCA_000146605.4_Turkey_5.1 NA na
Monodelphis_domestica 23 GCA_000002295.1 PRJNA12561 SAMN02953611 AAFR00000000.3 representative genome 13616 13616 Monodelphis domestica latest Chromosome Major Full 2007/01/25 MonDom5 The Genome Sequencing Platform, The Genome Assembly Team GCF_000002295.2 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/295/GCA_000002295.1_MonDom5 NA na
Mus_musculus 4 GCA_000001635.9 PRJNA20689 reference genome 10090 10090 Mus musculus strain=C57BL/6J latest Chromosome Major Full 2020/06/24 GRCm39 Genome Reference Consortium GCF_000001635.27 identical https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.9_GRCm39 NA na
Neoceratodus_forsteri 794647 GCA_016271365.1 PRJNA644903 SAMN15471169 JADMNL000000000.1 representative genome 7892 7892 Neoceratodus forsteri LF-2020 latest Chromosome Major Full 2020/12/28 neoFor_v3 University of Konstanz na na https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/271/365/GCA_016271365.1_neoFor_v3 NA na
Notamacropus_eugenii 75 GCA_000004035.1 PRJNA12587 ABQO000000000.1 representative genome 9315 9315 Notamacropus eugenii latest Scaffold Major Full 2009/11/06 Meug_1.1 Tammar Wallaby Genome Sequencing Consortium na na https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/004/035/GCA_000004035.1_Meug_1.1 NA na
Oreochromis_niloticus 83287 GCA_001858045.3 PRJNA344471 SAMN05859795 MKQE00000000.2 representative genome 8128 8128 Oreochromis niloticus F11D_XX latest Chromosome Major Full 2018/06/29 O_niloticus_UMD_NMBU University of Maryland GCF_001858045.2 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/858/045/GCA_001858045.3_O_niloticus_UMD_NMBU NA na
Ornithorhynchus_anatinus 194658 GCA_004115215.4 PRJNA489114 SAMN08537700 RZJT00000000.2 representative genome 9258 9258 Ornithorhynchus anatinus Pmale09 latest Chromosome Major Full 2020/11/06 mOrnAna1.pri.v4 Vertebrate Genomes Project GCF_004115215.2 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/115/215/GCA_004115215.4_mOrnAna1.pri.v4 NA na
Petromyzon_marinus 533746 GCA_010993605.1 PRJNA562011 SAMN12629506 JAAIYE000000000.1 representative genome 7757 7757 Petromyzon marinus kPetMar1 latest Chromosome Major Full 2020/02/24 kPetMar1.pri Vertebrate Genomes Project GCF_010993605.1 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/993/605/GCA_010993605.1_kPetMar1.pri NA na
Rana_temporaria 1484741 GCA_905171775.1 PRJEB42171 SAMEA7521635 CAJIMO000000000.1 representative genome 8407 8407 Rana temporaria latest Chromosome Major Full 2021/01/28 aRanTem1.1 Wellcome Sanger Institute GCF_905171775.1 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/171/775/GCA_905171775.1_aRanTem1.1 NA na
Scyliorhinus_canicula 1453583 GCA_902713615.2 PRJEB35945 SAMEA994730 CACTIT000000000.2 representative genome 7830 7830 Scyliorhinus canicula latest Chromosome Major Full 2021/01/28 sScyCan1.2 Wellcome Sanger Institute na na https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/713/615/GCA_902713615.2_sScyCan1.2 NA na
Taeniopygia_guttata 428230 GCA_008822105.2 PRJNA555095 SAMN09946140 VOHI00000000.2 na 59729 59729 Taeniopygia guttata Blue55 latest Chromosome Major Full 2020/02/21 bTaeGut2.pat.W.v2 Vertebrate Genomes Project GCF_008822105.2 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/008/822/105/GCA_008822105.2_bTaeGut2.pat.W.v2 superseded by newer assembly for species NA na
Takifugu_rubripes 1419030 GCA_901000725.3 PRJEB31988 SAMEA104384834 CAAJGN000000000.3 representative genome 31033 31033 Takifugu rubripes latest Chromosome Major Full 2021/04/24 fTakRub1.3 Wellcome Sanger Institute na na https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/901/000/725/GCA_901000725.3_fTakRub1.3 NA na
Xenopus_tropicalis 80 GCA_000004195.4 PRJNA577946 SAMN13041969 AAMC00000000.4 representative genome 8364 8364 Xenopus tropicalis strain=Nigerian latest Chromosome Major Full 2019/11/14 UCB_Xtro_10.0 University of California, Berkeley GCF_000004195.4 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/004/195/GCA_000004195.4_UCB_Xtro_10.0 NA na

Orthology

Orthologous genes were inferred using BUSCO.

Location of BUSCO results:

results/orthology/busco

Used BUSCO set: vertebrata_odb10

Total number of BUSCO genes in BUSCO set: 20
Number of BUSCO genes recovered in too few (20) samples: 3
BUSCO genes below threshold:
228730at7742, 164538at7742, 320238at7742

Number of samples with single-copy BUSCO score below threshold (0.5): 0
Genomes below threshold:

species single_copy duplicated fragmented missing
Amblyraja_radiata 2999 71 98 186
Anolis_carolinensis 2861 22 169 302
Callorhinchus_milii 2976 34 131 213
Canis_lupus 3122 47 65 120
Danio_kyathit 3107 45 75 127
Dasypus_novemcinctus 2717 61 212 364
Eptatretus_burgeri 1612 59 490 1193
Gallus_gallus 3180 29 45 100
Homo_sapiens 2984 130 77 163
Latimeria_chalumnae 2795 30 279 250
Loxodonta_africana 3039 22 103 190
Meleagris_gallopavo 2872 19 205 258
Monodelphis_domestica 3049 142 76 87
Mus_musculus 3124 55 51 124
Neoceratodus_forsteri 2101 75 723 455
Notamacropus_eugenii 1169 29 514 1642
Oreochromis_niloticus 3275 20 25 34
Ornithorhynchus_anatinus 3075 36 141 102
Petromyzon_marinus 2275 59 193 827
Protopterus_annectens 2029 1130 105 90
Rana_temporaria 3088 74 76 116
Scyliorhinus_canicula 2977 102 106 169
Taeniopygia_guttata 3161 19 50 124
Takifugu_rubripes 3120 77 73 84
Xenopus_tropicalis 3231 34 30 59

Alignments

full

Location of alignment files:

results/alignments/full

Used aligner(s) and settings:
1. clustalo
Parsimony informative sites cutoff: 50

Number of alignments for clustalo: 16
Number of alignments for mafft: 16
Number of alignments for muscle: 16

Overview of individual full alignments:
clustalo
mafft
muscle
length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed
193525at7742_aligned.fas 652 25 179 617 35 675 25 180 641 34 690 25 178 655 35
359032at7742_aligned.fas 347 25 104 325 22 351 25 106 329 22 347 25 105 325 22
406935at7742_aligned.fas 292 25 75 276 16 299 25 80 283 16 305 25 81 289 16
97645at7742_aligned.fas 1237 24 290 1162 75 1310 24 287 1233 77 1399 24 291 1320 79
332227at7742_aligned.fas 554 23 169 508 46 552 23 168 506 46 565 23 166 519 46
361842at7742_aligned.fas 352 25 74 334 18 365 25 75 345 20 364 25 79 344 20
409625at7742_aligned.fas 244 25 69 234 10 244 25 67 232 12 246 25 67 234 12
33940at7742_aligned.fas 1351 25 102 1085 266 1394 25 111 1123 271 1397 25 103 1127 270
378120at7742_aligned.fas 266 25 116 216 50 277 25 118 227 50 291 25 105 241 50
409719at7742_aligned.fas 410 25 72 388 22 369 25 72 347 22 443 25 72 421 22
342641at7742_aligned.fas 364 25 127 324 40 368 25 130 327 41 374 25 128 333 41
403632at7742_aligned.fas 423 25 34 412 11 431 25 44 420 11 441 25 41 430 11
413149at7742_aligned.fas 232 25 75 226 6 245 25 86 239 6 236 25 78 230 6
353318at7742_aligned.fas 382 25 86 369 13 390 25 88 377 13 397 25 90 384 13
404316at7742_aligned.fas 262 25 66 221 41 256 25 66 215 41 271 25 65 230 41
42971at7742_aligned.fas 1327 23 448 1037 290 1351 23 462 1060 291 1372 23 464 1082 290

trimmed

Location of trimmed alignment files:

results/alignments/trimmed

Parsimony informative sites cutoff: 50


Number of trimmed alignments for clustalo-aliscore: 16
Number of trimmed alignments for clustalo-trimal: 16
Number of trimmed alignments for mafft-aliscore: 16
Number of trimmed alignments for mafft-trimal: 16
Number of trimmed alignments for muscle-aliscore: 16
Number of trimmed alignments for muscle-trimal: 16

Overview of individual trimmed alignments:
clustalo
clustalo
mafft
mafft
muscle
muscle
aliscore
trimal
aliscore
trimal
aliscore
trimal
alignment length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed
193525at7742_aligned_trimmed.fas 448 25 178 404 44 454 25 179 419 35 461 25 179 417 44 469 25 180 435 34 470 25 176 426 44 469 25 178 434 35
332227at7742_aligned_trimmed.fas 288 23 141 223 65 298 23 169 252 46 296 23 139 231 65 299 23 168 253 46 288 23 142 223 65 296 23 166 250 46
33940at7742_aligned_trimmed.fas 1114 25 101 801 313 1018 25 102 752 266 1129 25 110 808 321 1022 25 111 751 271 1105 25 102 786 319 1016 25 103 746 270
342641at7742_aligned_trimmed.fas 275 25 119 233 42 259 25 127 219 40 282 25 122 240 42 264 25 130 223 41 292 25 122 250 42 265 25 128 224 41
353318at7742_aligned_trimmed.fas 206 25 87 193 13 214 25 86 201 13 205 25 89 192 13 232 25 88 219 13 205 25 91 192 13 250 25 90 237 13
359032at7742_aligned_trimmed.fas 166 25 104 142 24 254 25 104 232 22 166 25 104 142 24 239 25 106 217 22 165 25 103 141 24 191 25 105 169 22
361842at7742_aligned_trimmed.fas 233 25 75 212 21 219 25 74 201 18 239 25 76 215 24 219 25 75 199 20 235 25 77 211 24 218 25 79 198 20
378120at7742_aligned_trimmed.fas 253 25 115 192 61 253 25 116 203 50 261 25 117 200 61 253 25 118 203 50 257 25 104 196 61 252 25 105 202 50
403632at7742_aligned_trimmed.fas 176 25 31 161 15 166 25 34 155 11 190 25 41 175 15 171 25 44 160 11 192 25 41 177 15 171 25 41 160 11
404316at7742_aligned_trimmed.fas 204 25 67 158 46 217 25 66 176 41 207 25 67 161 46 219 25 66 178 41 205 25 66 159 46 217 25 65 176 41
406935at7742_aligned_trimmed.fas 139 25 75 119 20 204 25 75 188 16 147 25 80 125 22 207 25 80 191 16 142 25 81 120 22 206 25 81 190 16
409625at7742_aligned_trimmed.fas 132 25 69 120 12 137 25 69 127 10 139 25 67 125 14 134 25 67 122 12 138 25 67 124 14 133 25 67 121 12
409719at7742_aligned_trimmed.fas 131 25 72 108 23 227 25 72 205 22 134 25 72 111 23 151 25 72 129 22 130 25 72 107 23 228 25 72 206 22
413149at7742_aligned_trimmed.fas 104 25 67 95 9 124 25 75 118 6 112 25 72 103 9 125 25 86 119 6 106 25 67 97 9 127 25 78 121 6
42971at7742_aligned_trimmed.fas 935 23 413 625 310 1016 23 448 726 290 943 23 415 632 311 998 23 462 707 291 926 23 415 616 310 1026 23 464 736 290
97645at7742_aligned_trimmed.fas 798 24 284 705 93 747 24 290 672 75 822 24 279 725 97 736 24 287 659 77 837 24 280 739 98 740 24 291 661 79

filtered

Location of filtered alignment files:

results/alignments/filtered

Parsimony informative sites cutoff: 50


Number of filtered alignments for clustalo-aliscore: 15
Number of filtered alignments for clustalo-trimal: 15
Number of filtered alignments for mafft-aliscore: 15
Number of filtered alignments for mafft-trimal: 15
Number of filtered alignments for muscle-aliscore: 15
Number of filtered alignments for muscle-trimal: 15

Overview of individual filtered alignments:
clustalo
clustalo
mafft
mafft
muscle
muscle
aliscore
trimal
aliscore
trimal
aliscore
trimal
alignment length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed
193525at7742_aligned_trimmed.fas 448 25 178 404 44 454 25 179 419 35 461 25 179 417 44 469 25 180 435 34 470 25 176 426 44 469 25 178 434 35
332227at7742_aligned_trimmed.fas 288 23 141 223 65 298 23 169 252 46 296 23 139 231 65 299 23 168 253 46 288 23 142 223 65 296 23 166 250 46
33940at7742_aligned_trimmed.fas 1114 25 101 801 313 1018 25 102 752 266 1129 25 110 808 321 1022 25 111 751 271 1105 25 102 786 319 1016 25 103 746 270
342641at7742_aligned_trimmed.fas 275 25 119 233 42 259 25 127 219 40 282 25 122 240 42 264 25 130 223 41 292 25 122 250 42 265 25 128 224 41
353318at7742_aligned_trimmed.fas 206 25 87 193 13 214 25 86 201 13 205 25 89 192 13 232 25 88 219 13 205 25 91 192 13 250 25 90 237 13
359032at7742_aligned_trimmed.fas 166 25 104 142 24 254 25 104 232 22 166 25 104 142 24 239 25 106 217 22 165 25 103 141 24 191 25 105 169 22
361842at7742_aligned_trimmed.fas 233 25 75 212 21 219 25 74 201 18 239 25 76 215 24 219 25 75 199 20 235 25 77 211 24 218 25 79 198 20
378120at7742_aligned_trimmed.fas 253 25 115 192 61 253 25 116 203 50 261 25 117 200 61 253 25 118 203 50 257 25 104 196 61 252 25 105 202 50
404316at7742_aligned_trimmed.fas 204 25 67 158 46 217 25 66 176 41 207 25 67 161 46 219 25 66 178 41 205 25 66 159 46 217 25 65 176 41
406935at7742_aligned_trimmed.fas 139 25 75 119 20 204 25 75 188 16 147 25 80 125 22 207 25 80 191 16 142 25 81 120 22 206 25 81 190 16
409625at7742_aligned_trimmed.fas 132 25 69 120 12 137 25 69 127 10 139 25 67 125 14 134 25 67 122 12 138 25 67 124 14 133 25 67 121 12
409719at7742_aligned_trimmed.fas 131 25 72 108 23 227 25 72 205 22 134 25 72 111 23 151 25 72 129 22 130 25 72 107 23 228 25 72 206 22
413149at7742_aligned_trimmed.fas 104 25 67 95 9 124 25 75 118 6 112 25 72 103 9 125 25 86 119 6 106 25 67 97 9 127 25 78 121 6
42971at7742_aligned_trimmed.fas 935 23 413 625 310 1016 23 448 726 290 943 23 415 632 311 998 23 462 707 291 926 23 415 616 310 1026 23 464 736 290
97645at7742_aligned_trimmed.fas 798 24 284 705 93 747 24 290 672 75 822 24 279 725 97 736 24 287 659 77 837 24 280 739 98 740 24 291 661 79

Modeltesting

Location of modeltesting files:

results/modeltest
Overview of individual modeltest results:
alignment clustalo-aliscore clustalo-trimal mafft-aliscore mafft-trimal muscle-aliscore muscle-trimal
193525at7742 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4
332227at7742 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4
33940at7742 VT+R2 VT+R2 JTT+R2 JTT+R2 JTT+R2 JTT+R2
342641at7742 LG+I+G4 LG+I+G4 LG+I+G4 LG+I+G4 LG+I+G4 LG+I+G4
353318at7742 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4
359032at7742 LG+G4 JTT+I+G4 LG+G4 JTT+G4 LG+G4 JTT+G4
361842at7742 LG+G4 JTTDCMut+G4 LG+G4 JTTDCMut+G4 JTTDCMut+G4 JTTDCMut+G4
378120at7742 JTTDCMut+F+G4 JTTDCMut+F+R3 LG+G4 JTTDCMut+F+R3 LG+G4 LG+G4
404316at7742 JTT+R2 JTT+R3 JTT+R2 JTT+R3 JTT+R2 JTT+R3
406935at7742 LG+G4 VT+G4 LG+G4 LG+G4 LG+G4 VT+G4
409625at7742 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4
409719at7742 LG+G4 JTT+I+G4 LG+G4 JTTDCMut+G4 LG+G4 JTT+I+G4
413149at7742 JTTDCMut+G4 JTTDCMut+G4 JTTDCMut+G4 JTTDCMut+G4 WAG+G4 JTTDCMut+G4
42971at7742 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4
97645at7742 JTT+R3 JTT+R3 JTT+R3 JTT+R3 JTT+R3 JTT+R3

Genetrees

Location of gene trees:

results/modeltest

Overview of mean bootstrap values per gene-tree:
Total number of gene trees for clustalo-aliscore: 15
Total number of gene trees for clustalo-trimal: 15
Total number of gene trees for mafft-aliscore: 15
Total number of gene trees for mafft-trimal: 15
Total number of gene trees for muscle-aliscore: 15
Total number of gene trees for muscle-trimal: 15
gene clustalo-aliscore clustalo-trimal mafft-aliscore mafft-trimal muscle-aliscore muscle-trimal
193525at7742 85 87 85 87 85 87
332227at7742 84 87 82 85 76 85
33940at7742 81 83 84 84 80 80
342641at7742 78 76 77 77 78 77
353318at7742 81 82 80 81 79 84
359032at7742 79 79 78 79 79 80
361842at7742 81 79 78 78 77 78
378120at7742 77 73 77 73 78 77
404316at7742 79 81 82 85 76 79
406935at7742 68 74 68 79 75 78
409625at7742 73 74 81 85 79 82
409719at7742 68 78 68 73 66 73
413149at7742 74 78 78 79 81 79
42971at7742 86 86 84 86 85 88
97645at7742 84 85 83 83 83 84

MLtree

Location of phylogenetic results:

results/phylogeny-*/

Overview of concatenated Maximum-likelihood phylogenies:
software aligner trimmer boostraps bootstrap-cutoff ngenes tree
iqtree clustalo aliscore 1000 0 15
iqtree clustalo aliscore 1000 50 15
iqtree clustalo aliscore 1000 60 15
iqtree clustalo aliscore 1000 70 13
iqtree clustalo aliscore 1000 80 7
iqtree clustalo trimal 1000 0 15
iqtree clustalo trimal 1000 50 15
iqtree clustalo trimal 1000 60 15
iqtree clustalo trimal 1000 70 15
iqtree clustalo trimal 1000 80 7
iqtree mafft aliscore 1000 0 15
iqtree mafft aliscore 1000 50 15
iqtree mafft aliscore 1000 60 15
iqtree mafft aliscore 1000 70 13
iqtree mafft aliscore 1000 80 8
iqtree mafft trimal 1000 0 15
iqtree mafft trimal 1000 50 15
iqtree mafft trimal 1000 60 15
iqtree mafft trimal 1000 70 15
iqtree mafft trimal 1000 80 8
iqtree muscle aliscore 1000 0 15
iqtree muscle aliscore 1000 50 15
iqtree muscle aliscore 1000 60 15
iqtree muscle aliscore 1000 70 14
iqtree muscle aliscore 1000 80 5
iqtree muscle trimal 1000 0 15
iqtree muscle trimal 1000 50 15
iqtree muscle trimal 1000 60 15
iqtree muscle trimal 1000 70 15
iqtree muscle trimal 1000 80 8
raxmlng clustalo aliscore 100 0 15
raxmlng clustalo aliscore 100 50 15
raxmlng clustalo aliscore 100 60 15
raxmlng clustalo aliscore 100 70 13
raxmlng clustalo aliscore 100 80 7
raxmlng clustalo trimal 100 0 15
raxmlng clustalo trimal 100 50 15
raxmlng clustalo trimal 100 60 15
raxmlng clustalo trimal 100 70 15
raxmlng clustalo trimal 100 80 7
raxmlng mafft aliscore 100 0 15
raxmlng mafft aliscore 100 50 15
raxmlng mafft aliscore 100 60 15
raxmlng mafft aliscore 100 70 13
raxmlng mafft aliscore 100 80 8
raxmlng mafft trimal 100 0 15
raxmlng mafft trimal 100 50 15
raxmlng mafft trimal 100 60 15
raxmlng mafft trimal 100 70 15
raxmlng mafft trimal 100 80 8
raxmlng muscle aliscore 100 0 15
raxmlng muscle aliscore 100 50 15
raxmlng muscle aliscore 100 60 15
raxmlng muscle aliscore 100 70 14
raxmlng muscle aliscore 100 80 5
raxmlng muscle trimal 100 0 15
raxmlng muscle trimal 100 50 15
raxmlng muscle trimal 100 60 15
raxmlng muscle trimal 100 70 15
raxmlng muscle trimal 100 80 8

Speciestree

Location of phylogenetic results:

results/phylogeny-*/

Overview of species-tree phylogenies:
software aligner trimmer bootstrap-cutoff ngenes tree
astral clustalo aliscore 0 15
astral clustalo aliscore 50 15
astral clustalo aliscore 60 15
astral clustalo aliscore 70 13
astral clustalo aliscore 80 7
astral clustalo trimal 0 15
astral clustalo trimal 50 15
astral clustalo trimal 60 15
astral clustalo trimal 70 15
astral clustalo trimal 80 7
astral mafft aliscore 0 15
astral mafft aliscore 50 15
astral mafft aliscore 60 15
astral mafft aliscore 70 13
astral mafft aliscore 80 8
astral mafft trimal 0 15
astral mafft trimal 50 15
astral mafft trimal 60 15
astral mafft trimal 70 15
astral mafft trimal 80 8
astral muscle aliscore 0 15
astral muscle aliscore 50 15
astral muscle aliscore 60 15
astral muscle aliscore 70 14
astral muscle aliscore 80 5
astral muscle trimal 0 15
astral muscle trimal 50 15
astral muscle trimal 60 15
astral muscle trimal 70 15
astral muscle trimal 80 8

Log

## Sun Jan 22 20:27:17 CET 2023 - Setup: Will download species now - batch: 2
## Sun Jan 22 20:27:17 CET 2023 - Setup: Will download species now - batch: 3
## Sun Jan 22 20:27:17 CET 2023 - Setup: Will download species now - batch: 4
## Sun Jan 22 20:27:17 CET 2023 - Setup: Will download species now - batch: 5
## Sun Jan 22 20:27:17 CET 2023 - Setup: Will download species now - batch: 1
## Sun Jan 22 20:36:51 CET 2023 - phylociraptor setup done.
## Mon Jan 23 10:02:55 CET 2023 - Pipeline part 1 (orthology) done.
## Mon Jan 23 10:03:29 CET 2023 - BUSCO files will be filtered on a per-sample basis. This could lower the number of species in the final tree.
## Mon Jan 23 10:03:32 CET 2023 - Number of BUSCO sequence files: 16
## Mon Jan 23 10:03:32 CET 2023 - Number of deduplicated BUSCO sequence files: 16
## Mon Jan 23 10:03:32 CET 2023 - Pipeline part filter-orthology done.
## Mon Jan 23 10:04:35 CET 2023 - Pipeline part 2 (align) done.
## Mon Jan 23 10:04:51 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:51 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:53 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:53 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:56 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:56 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:59 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:59 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:59 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:04:59 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:05:00 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:00 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:00 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:05:00 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:02 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:02 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:02 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:02 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:02 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:03 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:03 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:05 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:05 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:13 CET 2023 - Number of alignments (muscle): 16
## Mon Jan 23 10:05:13 CET 2023 - Number of trimmed alignments (muscle - trimal): 16
## Mon Jan 23 10:05:13 CET 2023 - Number of alignments (muscle - trimal) after filtering: 15
## Mon Jan 23 10:05:17 CET 2023 - Number of alignments (mafft): 16
## Mon Jan 23 10:05:17 CET 2023 - Number of trimmed alignments (mafft - trimal): 16
## Mon Jan 23 10:05:18 CET 2023 - Number of alignments (mafft - trimal) after filtering: 15
## Mon Jan 23 10:05:19 CET 2023 - Number of alignments (clustalo): 16
## Mon Jan 23 10:05:19 CET 2023 - Number of trimmed alignments (clustalo - trimal): 16
## Mon Jan 23 10:05:19 CET 2023 - Number of alignments (clustalo - trimal) after filtering: 15
## Mon Jan 23 10:05:22 CET 2023 - Number of alignments (muscle): 16
## Mon Jan 23 10:05:22 CET 2023 - Number of trimmed alignments (muscle - aliscore): 16
## Mon Jan 23 10:05:22 CET 2023 - Number of alignments (muscle - aliscore) after filtering: 15
## Mon Jan 23 10:05:27 CET 2023 - Number of alignments (mafft): 16
## Mon Jan 23 10:05:27 CET 2023 - Number of trimmed alignments (mafft - aliscore): 16
## Mon Jan 23 10:05:27 CET 2023 - Number of alignments (mafft - aliscore) after filtering: 15
## Mon Jan 23 10:05:27 CET 2023 - Number of alignments (clustalo): 16
## Mon Jan 23 10:05:27 CET 2023 - Number of trimmed alignments (clustalo - aliscore): 16
## Mon Jan 23 10:05:27 CET 2023 - Number of alignments (clustalo - aliscore) after filtering: 15
## Mon Jan 23 10:05:32 CET 2023 - Pipeline part filter_align done.
## Mon Jan 23 10:15:03 CET 2023 - Pipeline part modeltest (model) done.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:53 CET 2023 - Speciestree reconstruction done.
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:29 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:29 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:29 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:29 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:30 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:30 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:30 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:31 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:32 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:32 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:32 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:33 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 10:26:33 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 10:26:33 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:33 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:34 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:36 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:36 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:36 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:47:57 CET 2023 - Pipeline part 3 (tree) done.
## Mon Jan 23 11:11:45 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:46 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:51 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:51 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:52 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:52 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:52 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:55 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:56 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:56 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:56 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:56 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:56 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 20:26:40 CET 2023 - Setup: Will download species now - batch: 4
## Mon Jan 23 20:26:40 CET 2023 - Setup: Will download species now - batch: 3
## Mon Jan 23 20:29:15 CET 2023 - Setup: Will download species now - batch: 5
## Mon Jan 23 20:31:04 CET 2023 - Setup: Will download species now - batch: 2
## Mon Jan 23 20:33:50 CET 2023 - Setup: Will download species now - batch: 1
## Mon Jan 23 21:16:42 CET 2023 - phylociraptor setup done.
## Mon Jan 23 21:25:22 CET 2023 - Pipeline part 1 (orthology) done.
## Mon Jan 23 21:31:37 CET 2023 - Pipeline part 1 (orthology) done.
## Mon Jan 23 21:32:30 CET 2023 - Pipeline part filter-orthology done.
## Mon Jan 23 22:03:55 CET 2023 - Pipeline part filter-orthology done.
## Mon Jan 23 22:06:03 CET 2023 - Pipeline part 2 (align) done.
## Mon Jan 23 22:06:21 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:21 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:21 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:21 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:22 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:22 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:23 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:23 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:23 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:23 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:24 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:24 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:24 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:24 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:25 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:26 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:26 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:26 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:27 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:27 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:27 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:27 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:29 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:29 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:29 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:29 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:29 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:30 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:31 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:31 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:33 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:34 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:34 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:35 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:35 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:35 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:36 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:36 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:36 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:36 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:44 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:44 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:44 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:45 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:45 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:45 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:45 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:45 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:51 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:51 CET 2023 - Number of alignments (mafft): 16
## Mon Jan 23 22:06:51 CET 2023 - Number of trimmed alignments (mafft - trimal): 16
## Mon Jan 23 22:06:51 CET 2023 - Number of alignments (mafft - trimal) after filtering: 15
## Mon Jan 23 22:06:53 CET 2023 - Number of alignments (clustalo): 16
## Mon Jan 23 22:06:53 CET 2023 - Number of trimmed alignments (clustalo - trimal): 16
## Mon Jan 23 22:06:53 CET 2023 - Number of alignments (clustalo - trimal) after filtering: 15
## Mon Jan 23 22:06:59 CET 2023 - Number of alignments (muscle): 16
## Mon Jan 23 22:06:59 CET 2023 - Number of trimmed alignments (muscle - trimal): 16
## Mon Jan 23 22:06:59 CET 2023 - Number of alignments (muscle - trimal) after filtering: 15
## Mon Jan 23 22:07:04 CET 2023 - Number of alignments (clustalo): 16
## Mon Jan 23 22:07:04 CET 2023 - Number of trimmed alignments (clustalo - aliscore): 16
## Mon Jan 23 22:07:04 CET 2023 - Number of alignments (clustalo - aliscore) after filtering: 15
## Mon Jan 23 22:07:05 CET 2023 - Number of alignments (mafft): 16
## Mon Jan 23 22:07:05 CET 2023 - Number of trimmed alignments (mafft - aliscore): 16
## Mon Jan 23 22:07:05 CET 2023 - Number of alignments (mafft - aliscore) after filtering: 15
## Mon Jan 23 22:07:07 CET 2023 - Number of alignments (muscle): 16
## Mon Jan 23 22:07:07 CET 2023 - Number of trimmed alignments (muscle - aliscore): 16
## Mon Jan 23 22:07:07 CET 2023 - Number of alignments (muscle - aliscore) after filtering: 15
## Mon Jan 23 22:07:15 CET 2023 - Pipeline part filter_align done.
## Mon Jan 23 22:17:01 CET 2023 - Pipeline part modeltest (model) done.
## Mon Jan 23 22:24:46 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:46 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:46 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:25:08 CET 2023 - Speciestree reconstruction done.
## Mon Jan 23 22:25:50 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 22:25:51 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:51 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:51 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 22:25:52 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 22:25:52 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 22:25:52 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 22:25:52 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:54 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 22:25:55 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:55 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:56 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:57 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 22:25:57 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 22:25:58 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:58 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:58 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 22:25:58 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 22:25:58 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 22:25:59 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:59 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:59 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:26:00 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:26:00 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:26:01 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:26:02 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:02 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:38:26 CET 2023 - Pipeline part 3 (tree) done.
## Mon Jan 23 22:40:59 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:41:00 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:00 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:03 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:03 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:03 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:03 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:09 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:09 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Tue Jan 24 21:05:06 CET 2023 - Pipeline part 3 (tree) done.
## Tue Jan 24 21:33:00 CET 2023 - Pipeline part ntree (njtree) done.